Regional campaing’s results (PhD Chapter 1)
Maps and figures
This series of files compile all analyses done during Chapter 1 for the regional campaign (2016).
All analyses have been done with PRIMER-e 6 and R 3.6.0.
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To assess analyses and regressions, click here.
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Caracteristics of each campaign
| 2014 | 2016 | 2017 | ||
|---|---|---|---|---|
| Sampling date | August-September | June to August | July | |
| Criteria for perturbation | Potentially impacted if close to the city or industries, References outside the bay | Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria | Human-impacted if in a region with a highly populated area, industries and maritime activities, Reference if none of these criteria | |
| Regions considered | BSI | BSI, CPC, BDA, MR | BSI, MR | |
| Number of sampled stations | 40 (20 HI, 20 R) | 78 (26 BSI, 19 CPC, 18 BDA, 15 MR) | 126 (111 BSI, 15 MR) | |
| Parameters sampled | Organic matter | yes | yes | yes |
| Photosynthetic pigments | no | yes | yes | |
| Sediment grain-size | yes | yes | yes | |
| Heavy-metals | yes | yes (for a limited number of stations) | no (interpolated based on 2014 and 2016 values) | |
| Benthic communities | Compartment targeted | Macro-infauna | Macro-infauna | Macro-infauna |
| Sieved used | 500 µm | 1 mm | 500 µm and 1 mm | |
| Conservation technique | Formaldehyle | Formaldehyle | Formaldehyle | |
| Others | N.A. | N.A. | N.A. |
We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.
Selected variables for the analyses:
- Depth of the station: depth (only for ANCOVAs)
- Percentage of organic matter: om
- Percentage of gravel: gravel
- Percentage of sand: sand
- Percentage of silt: silt
- Percentage of clay: clay
- Concentration of arsenic: arsenic
- Concentration of cadmium: cadmium
- Concentration of chromium: chromium
- Concentration of copper: copper
- Concentration of iron: iron
- Concentration of manganese: manganese
- Concentration of mercury: mercury
- Concentration of lead: lead
- Concentration of zinc: zinc
- Species richness: S
- Abundance of total individuals: N
- Shannon index: H
- Piélou evenness: J
Abundances of Mesodesma arctatum (Marc) and Cistenides granulata (Cgra) were also considered (see IndVal and SIMPER results).
As data is missing for metal concentrations outside BSI, two Designs have been used:
- Design 1: stations at BSI, CPC, BDA, MR with habitat parameters
- Design 2: stations at BSI with heavy metal concentrations.
Statistics for each variable considered:
| Â | Min | Max | Median | Mean | SD | SE | 95% CI |
|---|---|---|---|---|---|---|---|
| depth | 1.000 | 65.900 | 16.100 | 21.131 | 17.504 | 1.982 | 3.884 |
| om | 0.168 | 3.863 | 0.387 | 0.689 | 0.730 | 0.083 | 0.162 |
| gravel | 0.000 | 0.809 | 0.000 | 0.049 | 0.122 | 0.014 | 0.027 |
| sand | 0.000 | 1.001 | 0.873 | 0.707 | 0.348 | 0.039 | 0.077 |
| silt | 0.000 | 0.942 | 0.031 | 0.200 | 0.285 | 0.032 | 0.063 |
| clay | 0.000 | 0.497 | 0.006 | 0.043 | 0.098 | 0.011 | 0.022 |
| S | 0.000 | 13.000 | 4.000 | 4.795 | 2.969 | 0.336 | 0.659 |
| N | 0.000 | 142.000 | 12.000 | 19.846 | 25.867 | 2.929 | 5.740 |
| H | 0.000 | 2.307 | 1.069 | 1.080 | 0.610 | 0.069 | 0.135 |
| J | 0.000 | 1.000 | 0.838 | 0.724 | 0.292 | 0.033 | 0.065 |
| Â | Min | Max | Median | Mean | SD | SE | 95% CI |
|---|---|---|---|---|---|---|---|
| arsenic | 0.800 | 21.300 | 2.750 | 4.188 | 4.582 | 0.899 | 1.761 |
| cadmium | 0.080 | 0.270 | 0.145 | 0.152 | 0.047 | 0.009 | 0.018 |
| chromium | 17.000 | 111.000 | 42.500 | 49.385 | 23.565 | 4.621 | 9.058 |
| copper | 2.400 | 28.800 | 6.450 | 9.373 | 7.593 | 1.489 | 2.919 |
| iron | 21938.100 | 85408.600 | 42304.650 | 45356.633 | 16635.601 | 3262.510 | 6394.402 |
| manganese | 318.400 | 1657.100 | 711.450 | 776.662 | 348.066 | 68.261 | 133.790 |
| mercury | 0.007 | 0.091 | 0.019 | 0.023 | 0.017 | 0.003 | 0.006 |
| lead | 1.900 | 12.200 | 4.750 | 5.381 | 2.902 | 0.569 | 1.115 |
| zinc | 26.900 | 141.400 | 46.800 | 58.262 | 29.368 | 5.760 | 11.289 |
1. Maps
1.1. General map
1.2. Parameters maps
For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).
OM
Gravel
Sand
Silt
Clay
Arsenic
Cadmium
Chromium
Copper
Iron
Manganese
Mercury
Lead
Zinc
Cgra
Marc
Epar
Species richness
Total abundance
Shannon index
Piélou’s evenness
2. Figures
2.1. Barplots
Two types of barplots are available: one for the means by region, and one for the means by depth class. The latter have been done by classifying stations along three groups, based on their depth: shallow (0-10 m), medium (10-25 m) and deep (> 25 m). These thresholds are not supported by evidence, but allow to get a balanced design (26 stations for each depth class). However, we have been using PERMANOVA with depth as a covariate, instead of using these classes as a third factor.
Heavy metals are not presented here, as they were only sampled at BSI stations.
By regions
Organic matter
Grain-size
Species abundances
Diversity indices
By depth classes
Organic matter
Grain-size
Species abundances
Diversity indices
2.2. Phylum frequencies
| Phylum | BSI | CPC | BDA | MR |
|---|---|---|---|---|
| Annelida | 214 | 69 | 188 | 43 |
| Mollusca | 191 | 45 | 89 | 100 |
| Arthropoda | 119 | 13 | 30 | 43 |
| Echinodermata | 27 | 206 | 24 | 138 |
| Platyhelminthes | 3 | 0 | 0 | 0 |
| Nematoda | 2 | 0 | 0 | 0 |
| Nemertea | 1 | 0 | 0 | 0 |
| Brachiopoda | 0 | 0 | 0 | 2 |
| Cnidaria | 0 | 0 | 0 | 1 |
| Hemichordata | 0 | 0 | 0 | 0 |
| Phoronida | 0 | 0 | 0 | 0 |
2.3. Species estimation curves
2.4. Principal Component Analysis
Design 1
Variables have been scaled by mean and standard-deviation prior to analysis.
Design 2
Variables have been scaled by mean and standard-deviation prior to analysis.
Metals at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
2.5. Non-metric Multidimensional Scaling
Design 1
Variables have been scaled by mean and standard-deviation prior to analysis.
Design 2
Variables have been scaled by mean and standard-deviation prior to analysis.
Metals at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
Species
Stations with no species are deleted from this analysis.
2.6. Hierarchical Agglomerative Clustering
Design 1
Variables have been scaled by mean and standard-deviation prior to analysis.
## 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
## 1 2 2 2 2 2 2 2 2 2 3 3 2 3 2 1 3 2 2 2 2 2 2 2 2 2 2 1
## 72 73 74 75 76 77 78 79 80 82 83 86 87 88 90 92 93 94 95 96 97 98 99 100 101 102 103 104
## 1 1 1 2 1 2 2 2 3 3 3 2 2 2 3 1 3 2 1 3 1 3 1 1 3 2 3 3
## 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126
## 1 2 1 3 2 1 3 1 2 2 2 3 3 3 2 2 1 2 3 3 2 1
Design 2
Variables have been scaled by mean and standard-deviation prior to analysis.
## 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126
## 1 2 1 1 2 2 2 1 2 2 3 2 2 2 2 3 3 3 2 2 2 2 3 3 2 2
Metals at BSI
Variables have been scaled by mean and standard-deviation prior to analysis.
## 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126
## 1 2 1 1 3 3 3 1 3 3 3 3 3 3 3 3 2 2 3 3 3 3 3 2 3 3
Species
Stations with no species are deleted from this analysis.
## 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71
## 1 1 1 1 1 1 1 1 1 2 1 1 3 1 2 2 1 2 2 2 1 1 1 1 3 1 2 2
## 72 73 74 75 76 77 78 79 82 83 86 87 90 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106
## 1 1 2 2 1 1 2 2 1 3 1 2 1 2 3 3 1 1 3 1 3 3 1 1 1 1 1 1
## 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126
## 1 1 1 1 1 3 1 3 1 1 1 1 1 2 1 3 1 1 1 1